# R.E.DD.B. project F-58 # # Authors of the project: # F.-Y. Dupradeau, D. A. Case, C. Yu, R. Jimenez & F. E. Romesberg # # Please rename each tripos file: # tripos1.mol2 => HBA3.mol2 # tripos2.mol2 => HBA5.mol2 # tripos3.mol2 => HBA.mol2 # tripos4.mol2 => HBAN.mol2 # etc... logFile leap-mol2tooff.log alias e edit alias q quit alias c charge verbosity 2 HBA3 = loadmol2 HBA3.mol2 set HBA3 name "HBA3" set HBA3 head HBA3.1.P # tail = null set HBA3.1 connect0 HBA3.1.P set HBA3.1 connect1 HBA3.1.H3T set HBA3.1 restype nucleic set HBA3.1 name "HBA3" # set FF atom types set HBA3.1.P type P set HBA3.1.O1P type O2 set HBA3.1.O2P type O2 set HBA3.1.O5' type OS set HBA3.1.O3' type OH set HBA3.1.H3T type HO set HBA3.1.C5' type CT set HBA3.1.H5'1 type H1 set HBA3.1.H5'2 type H1 set HBA3.1.O4' type OS set HBA3.1.C4' type CT set HBA3.1.H4' type H1 set HBA3.1.C3' type CT set HBA3.1.H3' type H1 set HBA3.1.C2' type CT set HBA3.1.H2'1 type HC set HBA3.1.H2'2 type HC set HBA3.1.C1' type CT set HBA3.1.H1' type H1 set HBA3.1.N1 type NB set HBA3.1.C1 type CK set HBA3.1.O1 type OS set HBA3.1.C2B type CB set HBA3.1.C1B type CB set HBA3.1.C3B type CA set HBA3.1.H3B type HA set HBA3.1.C4B type CA set HBA3.1.H4B type HA set HBA3.1.C5B type CA set HBA3.1.H5B type HA set HBA3.1.C6B type CA set HBA3.1.H6B type HA set HBA3.1.C3A type CA set HBA3.1.H3A type HA set HBA3.1.C4A type CA set HBA3.1.H4A type HA set HBA3.1.C5A type CA set HBA3.1.C6A type CA set HBA3.1.H6A type HA set HBA3.1.C1A type CA set HBA3.1.C2A type C set HBA3.1.O2A type OH set HBA3.1.H2A type HO # save the OFF library saveoff HBA3 HBA3.off HBA5 = loadmol2 HBA5.mol2 set HBA5 name "HBA5" # head = null set HBA5 tail HBA5.1.O3' set HBA5.1 connect0 HBA5.1.H5T set HBA5.1 connect1 HBA5.1.O3' set HBA5.1 restype nucleic set HBA5.1 name "HBA5" # set FF atom types set HBA5.1.O5' type OH set HBA5.1.H5T type HO set HBA5.1.O3' type OS set HBA5.1.C5' type CT set HBA5.1.H5'1 type H1 set HBA5.1.H5'2 type H1 set HBA5.1.O4' type OS set HBA5.1.C4' type CT set HBA5.1.H4' type H1 set HBA5.1.C3' type CT set HBA5.1.H3' type H1 set HBA5.1.C2' type CT set HBA5.1.H2'1 type HC set HBA5.1.H2'2 type HC set HBA5.1.C1' type CT set HBA5.1.H1' type H1 set HBA5.1.N1 type NB set HBA5.1.C1 type CK set HBA5.1.O1 type OS set HBA5.1.C2B type CB set HBA5.1.C1B type CB set HBA5.1.C3B type CA set HBA5.1.H3B type HA set HBA5.1.C4B type CA set HBA5.1.H4B type HA set HBA5.1.C5B type CA set HBA5.1.H5B type HA set HBA5.1.C6B type CA set HBA5.1.H6B type HA set HBA5.1.C3A type CA set HBA5.1.H3A type HA set HBA5.1.C4A type CA set HBA5.1.H4A type HA set HBA5.1.C5A type CA set HBA5.1.C6A type CA set HBA5.1.H6A type HA set HBA5.1.C1A type CA set HBA5.1.C2A type C set HBA5.1.O2A type OH set HBA5.1.H2A type HO # save the OFF library saveoff HBA5 HBA5.off HBA = loadmol2 HBA.mol2 set HBA name "HBA" set HBA head HBA.1.P set HBA tail HBA.1.O3' set HBA.1 connect0 HBA.1.P set HBA.1 connect1 HBA.1.O3' set HBA.1 restype nucleic set HBA.1 name "HBA" # set FF atom types set HBA.1.P type P set HBA.1.O1P type O2 set HBA.1.O2P type O2 set HBA.1.O5' type OS set HBA.1.O3' type OS set HBA.1.C5' type CT set HBA.1.H5'1 type H1 set HBA.1.H5'2 type H1 set HBA.1.O4' type OS set HBA.1.C4' type CT set HBA.1.H4' type H1 set HBA.1.C3' type CT set HBA.1.H3' type H1 set HBA.1.C2' type CT set HBA.1.H2'1 type HC set HBA.1.H2'2 type HC set HBA.1.C1' type CT set HBA.1.H1' type H1 set HBA.1.N1 type NB set HBA.1.C1 type CK set HBA.1.O1 type OS set HBA.1.C2B type CB set HBA.1.C1B type CB set HBA.1.C3B type CA set HBA.1.H3B type HA set HBA.1.C4B type CA set HBA.1.H4B type HA set HBA.1.C5B type CA set HBA.1.H5B type HA set HBA.1.C6B type CA set HBA.1.H6B type HA set HBA.1.C3A type CA set HBA.1.H3A type HA set HBA.1.C4A type CA set HBA.1.H4A type HA set HBA.1.C5A type CA set HBA.1.C6A type CA set HBA.1.H6A type HA set HBA.1.C1A type CA set HBA.1.C2A type C set HBA.1.O2A type OH set HBA.1.H2A type HO # save the OFF library saveoff HBA HBA.off HBAN = loadmol2 HBAN.mol2 set HBAN name "HBAN" # head & tail = null set HBAN.1 connect0 HBAN.1.H5T set HBAN.1 connect1 HBAN.1.H3T set HBAN.1 restype nucleic set HBAN.1 name "HBAN" # set FF atom types set HBAN.1.O5' type OH set HBAN.1.H5T type HO set HBAN.1.O3' type OH set HBAN.1.H3T type HO set HBAN.1.C5' type CT set HBAN.1.H5'1 type H1 set HBAN.1.H5'2 type H1 set HBAN.1.O4' type OS set HBAN.1.C4' type CT set HBAN.1.H4' type H1 set HBAN.1.C3' type CT set HBAN.1.H3' type H1 set HBAN.1.C2' type CT set HBAN.1.H2'1 type HC set HBAN.1.H2'2 type HC set HBAN.1.C1' type CT set HBAN.1.H1' type H1 set HBAN.1.N1 type NB set HBAN.1.C1 type CK set HBAN.1.O1 type OS set HBAN.1.C2B type CB set HBAN.1.C1B type CB set HBAN.1.C3B type CA set HBAN.1.H3B type HA set HBAN.1.C4B type CA set HBAN.1.H4B type HA set HBAN.1.C5B type CA set HBAN.1.H5B type HA set HBAN.1.C6B type CA set HBAN.1.H6B type HA set HBAN.1.C3A type CA set HBAN.1.H3A type HA set HBAN.1.C4A type CA set HBAN.1.H4A type HA set HBAN.1.C5A type CA set HBAN.1.C6A type CA set HBAN.1.H6A type HA set HBAN.1.C1A type CA set HBAN.1.C2A type C set HBAN.1.O2A type OH set HBAN.1.H2A type HO # save the OFF library saveoff HBAN HBAN.off HBI3 = loadmol2 HBI3.mol2 set HBI3 name "HBI3" set HBI3 head HBI3.1.P # tail = null set HBI3.1 connect0 HBI3.1.P set HBI3.1 connect1 HBI3.1.H3T set HBI3.1 restype nucleic set HBI3.1 name "HBI3" # set FF atom types set HBI3.1.P type P set HBI3.1.O1P type O2 set HBI3.1.O2P type O2 set HBI3.1.O5' type OS set HBI3.1.O3' type OH set HBI3.1.H3T type HO set HBI3.1.C5' type CT set HBI3.1.H5'1 type H1 set HBI3.1.H5'2 type H1 set HBI3.1.O4' type OS set HBI3.1.C4' type CT set HBI3.1.H4' type H1 set HBI3.1.C3' type CT set HBI3.1.H3' type H1 set HBI3.1.C2' type CT set HBI3.1.H2'1 type HC set HBI3.1.H2'2 type HC set HBI3.1.C1' type CT set HBI3.1.H1' type H1 set HBI3.1.N1 type NB set HBI3.1.C1 type CK set HBI3.1.O1 type OS set HBI3.1.C2B type CB set HBI3.1.C1B type CB set HBI3.1.C3B type CA set HBI3.1.H3B type HA set HBI3.1.C4B type CA set HBI3.1.H4B type HA set HBI3.1.C5B type CA set HBI3.1.H5B type HA set HBI3.1.C6B type CA set HBI3.1.H6B type HA set HBI3.1.C3A type CA set HBI3.1.C4A type CA set HBI3.1.H4A type HA set HBI3.1.C5A type CA set HBI3.1.H5A type HA set HBI3.1.C6A type CA set HBI3.1.H6A type HA set HBI3.1.C1A type CA set HBI3.1.C2A type C set HBI3.1.O2A type OH set HBI3.1.H2A type HO # save the OFF library saveoff HBI3 HBI3.off HBI5 = loadmol2 HBI5.mol2 set HBI5 name "HBI5" # head = null set HBI5 tail HBI5.1.O3' set HBI5.1 connect0 HBI5.1.H5T set HBI5.1 connect1 HBI5.1.O3' set HBI5.1 restype nucleic set HBI5.1 name "HBI5" # set FF atom types set HBI5.1.O5' type OH set HBI5.1.H5T type HO set HBI5.1.O3' type OS set HBI5.1.C5' type CT set HBI5.1.H5'1 type H1 set HBI5.1.H5'2 type H1 set HBI5.1.O4' type OS set HBI5.1.C4' type CT set HBI5.1.H4' type H1 set HBI5.1.C3' type CT set HBI5.1.H3' type H1 set HBI5.1.C2' type CT set HBI5.1.H2'1 type HC set HBI5.1.H2'2 type HC set HBI5.1.C1' type CT set HBI5.1.H1' type H1 set HBI5.1.N1 type NB set HBI5.1.C1 type CK set HBI5.1.O1 type OS set HBI5.1.C2B type CB set HBI5.1.C1B type CB set HBI5.1.C3B type CA set HBI5.1.H3B type HA set HBI5.1.C4B type CA set HBI5.1.H4B type HA set HBI5.1.C5B type CA set HBI5.1.H5B type HA set HBI5.1.C6B type CA set HBI5.1.H6B type HA set HBI5.1.C3A type CA set HBI5.1.C4A type CA set HBI5.1.H4A type HA set HBI5.1.C5A type CA set HBI5.1.H5A type HA set HBI5.1.C6A type CA set HBI5.1.H6A type HA set HBI5.1.C1A type CA set HBI5.1.C2A type C set HBI5.1.O2A type OH set HBI5.1.H2A type HO # save the OFF library saveoff HBI5 HBI5.off HBI = loadmol2 HBI.mol2 set HBI name "HBI" set HBI head HBI.1.P set HBI tail HBI.1.O3' set HBI.1 connect0 HBI.1.P set HBI.1 connect1 HBI.1.O3' set HBI.1 restype nucleic set HBI.1 name "HBI" # set FF atom types set HBI.1.P type P set HBI.1.O1P type O2 set HBI.1.O2P type O2 set HBI.1.O5' type OS set HBI.1.O3' type OS set HBI.1.C5' type CT set HBI.1.H5'1 type H1 set HBI.1.H5'2 type H1 set HBI.1.O4' type OS set HBI.1.C4' type CT set HBI.1.H4' type H1 set HBI.1.C3' type CT set HBI.1.H3' type H1 set HBI.1.C2' type CT set HBI.1.H2'1 type HC set HBI.1.H2'2 type HC set HBI.1.C1' type CT set HBI.1.H1' type H1 set HBI.1.N1 type NB set HBI.1.C1 type CK set HBI.1.O1 type OS set HBI.1.C2B type CB set HBI.1.C1B type CB set HBI.1.C3B type CA set HBI.1.H3B type HA set HBI.1.C4B type CA set HBI.1.H4B type HA set HBI.1.C5B type CA set HBI.1.H5B type HA set HBI.1.C6B type CA set HBI.1.H6B type HA set HBI.1.C3A type CA set HBI.1.C4A type CA set HBI.1.H4A type HA set HBI.1.C5A type CA set HBI.1.H5A type HA set HBI.1.C6A type CA set HBI.1.H6A type HA set HBI.1.C1A type CA set HBI.1.C2A type C set HBI.1.O2A type OH set HBI.1.H2A type HO # save the OFF library saveoff HBI HBI.off HBIN = loadmol2 HBIN.mol2 set HBIN name "HBIN" # head & tail = null set HBIN.1 connect0 HBIN.1.H5T set HBIN.1 connect1 HBIN.1.H3T set HBIN.1 restype nucleic set HBIN.1 name "HBIN" # set FF atom types set HBIN.1.O5' type OH set HBIN.1.H5T type HO set HBIN.1.O3' type OH set HBIN.1.H3T type HO set HBIN.1.C5' type CT set HBIN.1.H5'1 type H1 set HBIN.1.H5'2 type H1 set HBIN.1.O4' type OS set HBIN.1.C4' type CT set HBIN.1.H4' type H1 set HBIN.1.C3' type CT set HBIN.1.H3' type H1 set HBIN.1.C2' type CT set HBIN.1.H2'1 type HC set HBIN.1.H2'2 type HC set HBIN.1.C1' type CT set HBIN.1.H1' type H1 set HBIN.1.N1 type NB set HBIN.1.C1 type CK set HBIN.1.O1 type OS set HBIN.1.C2B type CB set HBIN.1.C1B type CB set HBIN.1.C3B type CA set HBIN.1.H3B type HA set HBIN.1.C4B type CA set HBIN.1.H4B type HA set HBIN.1.C5B type CA set HBIN.1.H5B type HA set HBIN.1.C6B type CA set HBIN.1.H6B type HA set HBIN.1.C3A type CA set HBIN.1.C4A type CA set HBIN.1.H4A type HA set HBIN.1.C5A type CA set HBIN.1.H5A type HA set HBIN.1.C6A type CA set HBIN.1.H6A type HA set HBIN.1.C1A type CA set HBIN.1.C2A type C set HBIN.1.O2A type OH set HBIN.1.H2A type HO # save the OFF library saveoff HBIN HBIN.off q